Bioinformatik

This book presents novel statistics methods and reproducible software that helps to solve challenging problems in biomedicine. Specifically, it consists of a collection of 11 chapters contributed by some of the leading experts in the mathematical and statistical field which address new challenges in very disparate biomedical areas, such as genomics, cancer, circadian biology, microbiome, mental disorders, and more. The mathematical rigor is written in a user-friendly way to serve a general biomedical audience ranging from trainees or students to doctors, as well as scientific researchers, university departments, and PhD students.

This volume presents an array of different case studies which take as primary material data sourced from the NOW (¿New and Old Worlds¿) database of fossil mammals. The NOW database was one of the very first large paleobiological databases, and since 1996 it has been expanded from including mainly Neogene European land mammals to cover the entire Cenozoic at a global scale. In the last two decades the number of works that are based in the use of huge databases to explore ecological and evolutionary questions has increased exponentially, and even though the importance of big data in paleobiological research has been outlined in selected chapters of general works, no volume has appeared before this one which solely focuses on the databases as a primary source in reconstructing the past. The purpose of this book is to provide an illustrative volume showing the importance of big data in paleobiological research, and presenting a broad array of unpublished examples and case studies. The book is mainly aimed to professional palaeobiologists working with Cenozoic land mammals, but the scope of the book is broad enough to fit the interest for evolutionary biologists, paleoclimatologists and paleoecologists.The volume is divided in four parts. The first part includes two chapters on the development of large paleobiological databases, providing a first-hand account on the logic and the functioning of these databases. This is a much-needed perspective which is ignored by most researchers and users of such databases and, even if centered in the NOW database, the lessons that can be learned from this part can be extended to other examples. After this introductory part, the body of the book follows and is divided into three parts: patterns in regional faunas; large scale patterns and processes; and ecological, biogeographical and evolutionary patterns of key taxa. Each chapter is written by well-known specialists in the field, withsome participation of members of the NOW advisory board. The array of selected mammal taxa ranges from carnivores, equids, ruminants and rodents to the genus Homo. The topics studied also include the diversification and radiation of major clades, large-scale paleobiogeographical patterns, the evolution of ecomorphological patterns and paleobiological problems such as evolution of body size or species longevity. In most cases the results are discussed in relation to protracted environmental or paleogeographic changes.

Handbook of MRI Pulse Sequences, Second Edition includes 92 self-contained sections, with each section focusing on a single subject. A new section on detailing the advanced pulse sequence techniques covers a variety of basic and advanced image reconstruction methods. The extensive topic coverage and cross-referencing makes this book ideal for beginners learning the building blocks of MRI pulse sequence design, as well as for experienced professionals who are seeking deeper knowledge of a particular technique. This book is among the most important medical imaging techniques available today. Each of these scanners is capable of running many different "pulse sequences." These sequences are governed by physics and engineering principles and implemented by software programs that control the MRI hardware.

This book gathers selected, extended and revised contributions to the 17th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering and the 5th Conference on Imaging and Visualization (CMBBE 2021), held online on September 7-9, 2021, from Bonn, Germany. It reports on cutting-edge models, algorithms and imaging techniques for studying cells, tissues and organs in normal and pathological conditions. It covers numerical and machine learning methods, finite element modeling and virtual reality techniques, applied to understand biomechanics of movement, fluid and soft tissue biomechanics. It also reports on related advances in rehabilitation, surgery and diagnosis. All in all, this book offers a timely snapshot of the latest research and current challenges at the interface between biomedical engineering, computational biomechanics and biological imaging. Thus, it is expected to provide a source of inspiration for future research and cross-disciplinary collaborations.

Quantitative ultrasound (QUS) continues to mature as a research field and is primed to make a swift transition to routine preclinical and clinical applications. This book will serve two main purposes:Advanced education in QUS by providing a complete and thorough review of all theoretical, physical, and engineering aspects of QUS.Review of recent development of QUS by lead contributors in the research field.This 2nd edition will focus on 6 modern research topics related to quantitative ultrasound of soft tissues:Spectral-based methods for tissue characterization, tissue typing, cancer detection, etc.Attenuation estimation for tissue characterization and improving spectral based methodsEnvelope statistics analysis as a means of quantifying and imaging tissue properties.Ultrasound computed tomography for preclinical and clinical imaging.Scanning acoustic microscopy for formingimages of mechanical properties of soft tissues with micron resolution.Phantoms for quantitative ultrasound.

This volume gathers together selected peer-reviewed works presented at the BIOMAT 2022 International Symposium, which was virtually held on November 7-11, 2022, with an organization staff based in Rio de Janeiro, Brazil.Topics touched on in this volume include infection spread in a population described by an agent-based approach; the study of gene essentiality via network-based computational modeling; stochastic models of neuronal dynamics; and the modeling of a statistical distribution of amino acids in protein domain families. The reader will also find texts in epidemic models with dynamic social distancing; with no vertical transmission; and with general incidence rates. Aspects of COVID-19 dynamics: the use of an SEIR model to analyze its spread in Brazil; the age-dependent manner of modeling its spread pattern; the impact of media awareness programs; and a web-based computational tool for Non-invasive hemodynamics evaluation of coronary stenosis are also covered.Held every year since 2001, The BIOMAT International Symposium gathers together, in a single conference, researchers from Mathematics, Physics, Biology, and affine fields to promote the interdisciplinary exchange of results, ideas and techniques, promoting truly international cooperation for problem discussion. BIOMAT volumes published from 2017 to 2021 are also available by Springer.

This book presents the applications of systems biology and synthetic biology in cancer medicine. It highlights the use of computational and mathematical models to decipher the complexity of cancer heterogeneity. The book emphasizes the modeling approaches for predicting behavior of cancer cells, tissues in context of drug response, and angiogenesis. It introduces cell-based therapies for the treatment of various cancers and reviews the role of neural networks for drug response prediction. Further, it examines the system biology approaches for the identification of medicinal plants in cancer drug discovery. It explores the opportunities for metabolic engineering in the realm of cancer research towards development of new cancer therapies based on metabolically derived targets. Lastly, it discusses the applications of data mining techniques in cancer research. This book is an excellent guide for oncologists and researchers who are involved in the latest cancer research.

This volume presents a collection of versatile methodologies to investigate prokaryotic gene regulation, with focus on the different levels of information processing and usefulness for various model organisms, whether archaeal, bacterial, or both. The chapters in this book are divided into four sections. Section One covers methods that enable the study of the structure of the bacterial/archaeal chromosome, the main template for all gene regulatory processes, and its epigenetic modification. Section Two looks at a selection of approaches that enable higher levels of understanding of transcription initiation, a key step in information processing. Section Three discusses the investigation of regulating transcription factors, which are often considered the main players in gene regulation in prokaryotic cells. The Fourth Section focuses on the next stage of information processing at which gene regulation occurs, namely the RNA-based level. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Cutting-edge and comprehensive, Prokaryotic Gene Regulation: Methods and Protocols is a valuable resource for researchers interested in learning more about this diverse field.

This book presents methods and tools of network biology and bioinformatics for understanding the disease dynamics and identification of drug targets. The initial section of chapters introduce the theoretical aspects followed by the different applications for construction and analysis of biological networks, methods for identifying crucial nodes in networks, and network dynamics. The book covers the latest advances in the network medicine, exploring the different types of biological networks, and their applications. It further reviews the role of R language in the network-based approaches that help in understanding biological systems and identifying biological functions. Towards the end, the book explores the recent developments and applications in machine learning and its potential for advancing network biology. Finally, the book elucidates a comprehensive yet a representative description of challenges associated with the understanding of disease dynamics using network biology. Given its scope, the book is intended for researchers and advanced postgraduate students of bioinformatics, computational biology, and medical sciences.¿

This book provides an interdisciplinary look at emerging trends in signal processing and biomedicine found at the intersection of healthcare, engineering, and computer science. Bringing together expanded versions of selected papers presented at the 2020 IEEE Signal Processing in Medicine and Biology Symposium (IEEE SPMB), it examines the vital role signal processing plays in enabling a new generation of technology based on big data and looks at applications ranging from medical electronics to data mining of electronic medical records. Topics covered include analysis of medical images, machine learning, biomedical nanosensors, wireless technologies, and instrumentation and electrical stimulation. Biomedical Sensing and Analysis: Signal Processing in Medicine and Biology presents tutorials and examples of successful applications, and will appeal to a wide range of professionals, researchers, and students interested in applications of signal processing, medicine, and biology.Presents an interdisciplinary look at research trends in signal processing and biomedicine;Promotes collaboration between healthcare practitioners and signal processing researchers;Includes tutorials and examples of successful applications.

This monograph contains an in-depth and coherent treatment of dimension-reduced modeling of blood flows on the level of large vessels (macrocirculation). The authors reduce the complexity by combining a one-dimensional Navier-Stokes equation and a simplified FSI-concept. The influence of omitted vessels, which are subsequent to the outlets of larger vessels, is accounted for by systems of ordinary differential equations (0D models). The target audience primarily comprises research experts in the field of biomedical engineering, but the book may also be beneficial for graduate students alike.

This book constitutes the refereed proceedings of the 20th Annual RECOMB Satellite Workshop on Comparative Genomics, RECOMB-CG 2023 which took place in Istanbul, Turkey, in April 2023. The 15 full papers included in this book were carefully reviewed and selected from 25 submissions. The papers present cutting edge research in comparative genomics, with an emphasis on computational approaches and novel experimental results.Chapters "Inferring Clusters of Orthologous and Paralogous Transcripts" and "Gene Order Phylogeny via Ancestral Genome Reconstruction under Dollo" are published Open Access under Creative Commons Attribution license (CC BY 4.0).

This book aims to promote the interaction among the scientific community to discuss applications of CS/AI with an interdisciplinary character, exploring the interactions between sub-areas of CS/AI, bioinformatics, chemoinformatics, and systems biology. The success of bioinformatics in recent years has been prompted by research in molecular biology and molecular medicine in several initiatives. This year¿s technical program presents both high quality and diversity, with contributions in well-established and evolving areas of research. The PACBB¿23 technical program has selected 9 full papers in the main track and, as in past editions, it will be special issues in ranked journals. This symposium is organized by the LASI and Centro Algoritmi of the University of Minho (Portugal). The authors would like to thank all the contributing authors, the members of the program committee, national associations (AEPIA, APPIA), and the sponsors (AIR Institute).

This volume details the development of updated dry lab and wet lab based methods for the reconstruction of Gene regulatory networks (GRN). Chapters guide readers through culprit genes, in-silico drug discovery techniques, genome-wide ChIP-X data, high-Throughput Transcriptomic Data Exome Sequencing, Next-Generation Sequencing, Fuorescence Spectroscopy, data analysis in Bioinformatics, Computational Biology, and S-system based modeling of GRN. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.Authoritative and cutting-edge, Reverse Engineering of Regulatory Networks aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.

This second edition provides new and updated methods and techniques for identification of drug target, binding sites prediction, high- throughput virtual screening, lead discovery and optimization, conformational sampling, prediction of pharmacokinetic properties using computer-based methodologies. Chapters also focus on the application of the latest artificial intelligence technologies for computer aided drug discovery. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Computational Drug Discovery and Design, Second Edition aims to effectively utilize computational methodologies in discovery and design of novel drugs.

This detailed book presents recent methodologies for the task of inspecting the genomic world of plants, extracting valuable information, and presenting it in a readable way. With a focus on bioinformatics tools, the volume explores phylogenetics and evolution, Omics analysis, as well as experimental procedures for trait characterization. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of vital expert implementation advice that will lead to successful results. Authoritative and practical, Plant Comparative Genomics serves as an ideal resource for researchers looking to implement comparative tools in order to explore their genomic data for their daily scientific work.

"This volume introduces researchers to the idea of no-boundary thinking (NBT) in biological and biomedical research. Written by a team of specialists, drawing on their own experience, it provides a guide to integrating and synthesizing data and knowledge from bioinformatics to define important problems and articulate impactful research questions"--

This book reviews new promising drug targets for Neglected Tropical Diseases (NTDs), with a special focus on antiprotozoal drugs against trpyanosomatids Trypanosoma cruzi and Leishmania spp. The book offers a comprehensive overview of the most recent studied targets, and it outlines classical and new treatments and delivery strategies. Expert contributors describe new methods of analysis and bio-prospecting for new compounds, and provide a critical perspective of the translational process used in the research and development of new drug candidates.The book will appeal not only to researchers, students and professionals interested in drug development to protozoan diseases, but also to medicinal chemists in general.

Sensitive periods occur when unique experiences permanently influence brain development either by their presence or absence. This volume covers underlying brain systems and behaviors that are sculpted by the environment in humans and animals in a search for commonalities. The mechanisms involved, the importance of timing in the process, and factors that can change the brain are discussed in this exciting book. Different chapters examine how experience guides the development of cells, circuits, and function using vision, cortical circuits, and cognition as frameworks. Scientific evidence for effective preventative intervention approaches, including diet, exercise, and music, are included to find ways to maximize child and adolescent development. The adverse effects of early brain injury are also included. As sensitive periods are gaining importance in their application in the real-world, novel statistical approaches for human studies are presented and the importance of sensitive periods are covered by examining the juvenile justice system. The book has interdisciplinary appeal and scholars with an interest in brain resiliency or vulnerability will find it of particular interest.

This volume provides practical guidance on a variety of techniques and steps to ensure successful variant calling. Chapters detail methods for variant calling from single-nucleotide variants to structural variants, variant calling in specialized data types such as RNA-seq and UMI-tagged sequencing, alignment-free genotyping and SNP calling, variant detection in single-cell DNA sequencing data, variant annotation, and preanalytical quality control to ensure successful variant calling. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists step-by-step protocol to execute the algorithms, describes the input and output data, and includes tips on troubleshooting and known pitfalls. Authoritative and cutting-edge, Variant Calling: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.  

This volume describes computational approaches to predict multitudes of PTM sites. Chapters describe in depth approaches on algorithms, state-of-the-art Deep Learning based approaches, hand-crafted features, physico-chemical based features, issues related to obtaining negative training, sequence-based features, and structure-based features. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Authoritative and cutting-edge,  Computational Methods for Predicting Post-Translational Modification Sites aims to be a useful guide for researchers who are interested in the field of PTM site prediction. 

This volume details step-by-step instructions on biomedical literature mining protocols. Chapters guide readers through various topics such as, disease comorbidity, literature-based discovery, protocols to combine literature mining, machine learning for predicting biomedical discoveries, and uncovering unknown public knowledge by combining two pieces of information from different sets of PubMed articles. Additional chapters discuss the importance of data science to understand outbreaks such as COVID-19.   Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Biomedical Text Mining aims to be a useful practical guide to researches to help further their studies.          

This monograph presents the results of over 10 years of paleontological and geological survey in the Baynunah Formation of the United Arab Emirates. Exposed widely in western Abu Dhabi Emirate, the Baynunah Formation and its fossils provide the only record of terrestrial environments and evolution in the Arabian Peninsula during the late Miocene epoch (12-5 Ma).This volume describes new fossils collected since 2002, presented systematically by taxon, and including mammals, reptiles, and invertebrates, as well as fossil trackways. The discoveries are framed within the results of new geological, geochemical, and geochrononological analyses, providing an updated and synthetic view of the age, environments, and biogeographic relationships of this important fossil assemblage.

Mining Biomedical Text, Images and Visual Features for Information Retrieval provides broad coverage of the concepts, themes, and instrumentalities of the important, evolving area of biomedical text, images, and visual features towards information retrieval. The book aims to encourage an even wider adoption of IR methods for assisting in problem-solving and to stimulate research that may lead to additional innovations in this area of research. Topics covered include Internet of Things for health informatics; data privacy; smart healthcare; medical image processing; 3D medical images; evolutionary computing; deep learning; medical ontology; linguistic indexing; lexical analysis; and domain specific semantic categories in biomedical applications. This is a valuable resource for researchers and graduate students who are interested to learn more about data mining techniques to improve their research work.

Next Generation eHealth: Applied Data Science, Machine Learning and Extreme Computational Intelligence discusses the emergence, the impact, and the potential of sophisticated computational capabilities in healthcare. This book provides useful therapeutic targets to improve diagnosis, therapies, and prognosis of diseases, as well as helping with the establishment of better and more efficient next-generation medicine and medical systems. Machine learning as a field greatly contributes to next-generation medical research with the goal of improving medicine practices and medical Systems. As a contributing factor to better health outcomes, this book highlights the need for advanced training of professionals from various health areas, clinicians, educators, and social professionals who deal with patients. Content illustrates current issues and future promises as they pertain to all stakeholders, including informaticians, professionals in diagnostics, key industry experts in biotech, pharma, administrators, clinicians, patients, educators, students, health professionals, social scientists and legislators, health providers, advocacy groups, and more. With a focus on machine learning, deep learning, and neural networks, this volume communicates in an integrated, fresh, and novel way the impact of data science and computational intelligence to diverse audiences.

Reverse Vaccinology: Concept, Methods, and Advancement presents the development strategy of new vaccines through genome sequencing bioinformatics analysis. This book promises to revolutionize vaccine development, especially for pathogens to which the classical applications of Pasteur’s principles have failed, and it is explained in detail in this book.This book is split into three sections: the first, Concept, brings the basis of reverse vaccinology, vaccine antigen discovery, and subunit vaccine; the second, Tools and Methods, describes immunoinformatic, proteomics for epitope-vaccine design, databases, network analysis, machine learning, and NGS-driven antigen screening technology; and the last one, Disease Case Study, discusses real-world examples in the development of new vaccines for diverse diseases.It is a valuable resource for bioinformaticians, researchers, students, and members of the biomedical and medical fields who want to learn more about a new and agile process for the development of new vaccines.

This volume discusses the latest online plant genomics and cytogenetic resources used by plant evolutionary biologists and plant breeders. The chapters in this book are organized into two parts. Part One looks at plant genomic databases, and covers topics such as plant phenomics and genomics research data repositories, InpactorDB, PlanTEenrichment, and PEATmoss, among others. Part Two looks at cytogenetics and chromosome-related databases, and covers resources such as the Plant DNA C-values database, the Delphineae Chromosome Database (DCDB), B-chrom, a Database on B-chromosomes, and the Plant Ribosomal DNA Database. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective databases and offers explicit directions on how to access and get the most of these resources. Cutting-edge and comprehensive, Plant Genomic and Cytogenetic Databases is a valuable instrument for any plant science researcher who is interested in learning more about the wealth of information that is available through the use of these databases.

This detailed collection explores genome-wide association studies (GWAS), which have revolutionized the investigation of complex traits over the past decade and have unveiled numerous useful genotype-phenotype associations in plants. The book describes the key concepts and methods underlying GWAS, including the genetic architecture underlying variation for phenotypic traits, the structure of genetic variation in plants, technologies for capturing genetic information, study designs, and the statistical models and bioinformatics tools used for data analysis. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of invaluable implementation advice that leads to the most fruitful research results. Authoritative and practical, Genome-Wide Association Studies serves as an extremely valuable resource for the plant research community by rendering GWAS analysis less challenging and more accessible to a broader group of users.